Contacts of the helix formed by residues 138 - 154 (chain A) in PDB entry 6B5G
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 138 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A GLN* 2.9 27.2 + - + +
136A PHE 3.5 0.2 - - - -
137A TYR* 1.3 83.7 - - + +
139A ASP* 1.3 76.7 + - - +
141A GLN* 3.4 4.0 + - - +
142A GLY* 2.9 20.3 + - - -
314A PHE* 4.0 19.1 - - + -
602A CQY 4.0 54.3 - - + +
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Residues in contact with ASP 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A GLU* 4.2 8.6 - - + +
130A LYS* 3.0 42.3 + - - +
134A GLN* 3.3 11.7 + - - +
135A ALA* 3.5 13.9 - - + +
138A VAL* 1.3 80.2 - - - +
140A LEU* 1.3 65.4 + - + +
142A GLY* 2.9 5.7 + - - -
143A VAL* 2.9 32.4 + - + +
188A PHE* 3.0 28.9 - - + -
190A LEU* 6.1 0.4 - - + -
191A LEU* 4.4 14.3 - - + +
314A PHE* 5.1 1.6 - - - -
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Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A VAL* 3.6 30.5 - - + -
117A ARG* 3.9 31.2 - - + +
120A LEU* 3.9 13.7 - - + +
121A ALA* 3.9 18.8 - - + +
124A GLU* 4.4 9.0 - - + -
135A ALA 2.9 23.1 + - - +
136A PHE 3.5 10.3 + - - +
138A VAL 3.5 0.2 - - - -
139A ASP* 1.3 78.8 - - + +
141A GLN* 1.3 62.8 + - - +
143A VAL* 3.2 4.3 + - + +
144A ILE* 3.1 31.1 + - - +
190A LEU* 3.8 27.1 - - + -
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Residues in contact with GLN 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ARG* 3.7 20.0 - - - +
136A PHE 3.8 4.8 + - - -
137A TYR* 3.1 29.1 + - - +
138A VAL* 3.4 2.4 + - - +
139A ASP 3.2 0.4 - - - -
140A LEU* 1.3 79.3 - - - +
142A GLY* 1.3 58.5 + - - +
144A ILE* 3.4 6.7 + - + +
145A LYS* 2.9 66.2 + - + +
602A CQY 5.0 7.1 - - - +
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Residues in contact with GLY 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A VAL 2.9 11.5 + - - -
139A ASP 2.9 9.3 + - - -
141A GLN* 1.3 77.4 - - - +
143A VAL* 1.3 55.2 + - - +
145A LYS* 4.1 6.2 - - - +
146A THR* 2.6 32.4 + - - -
191A LEU* 3.3 16.4 - - - +
602A CQY 4.7 11.0 + - - -
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Residues in contact with VAL 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A VAL* 4.0 18.6 - - + -
139A ASP 2.9 19.6 + - - +
140A LEU* 3.6 9.0 - - + +
141A GLN 3.2 0.4 - - - -
142A GLY* 1.3 76.2 - - - +
144A ILE* 1.3 66.8 + - - +
146A THR* 3.3 3.5 + - - -
147A PHE* 3.2 45.2 + - + -
190A LEU* 3.7 31.9 - - + +
191A LEU* 3.7 30.3 - - - +
194A ALA* 4.1 7.9 - - + -
222A MET* 5.5 0.4 - - + -
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Residues in contact with ILE 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ALA* 3.8 19.3 - - + +
113A VAL* 3.6 22.0 - - + -
114A GLU* 3.8 44.4 - - - +
117A ARG* 4.1 20.9 - - + +
140A LEU 3.1 20.9 + - - +
141A GLN* 4.0 5.2 - - + +
143A VAL* 1.3 76.1 - - - +
145A LYS* 1.3 61.0 + - + +
147A PHE* 3.5 1.5 + - - -
148A ARG* 3.1 56.2 + - + +
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Residues in contact with LYS 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A GLN* 2.9 52.5 + - + +
142A GLY* 4.5 4.9 - - - +
144A ILE* 1.3 77.6 - - + +
146A THR* 1.3 60.5 + - - +
148A ARG* 4.0 6.4 - - + +
149A TYR* 2.8 31.7 + - - +
479A ALA* 4.3 10.2 - - + +
165C ASP* 3.2 30.9 + - - +
98D ASP* 4.5 5.7 + - - -
100D SER* 5.1 5.4 - - - +
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Residues in contact with THR 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A GLY 2.6 23.3 + - - -
143A VAL 3.3 5.4 + - - -
145A LYS* 1.3 79.6 - - - +
147A PHE* 1.3 62.6 + - - +
149A TYR* 3.3 0.7 + - - +
150A TYR* 3.1 34.3 + - + -
191A LEU* 4.0 0.2 - - - +
194A ALA* 3.8 34.1 - - + +
195A TRP* 3.6 25.2 + - + -
198A ALA* 3.9 9.2 - - + -
479A ALA* 4.5 12.6 - - - +
495A MET* 4.5 6.9 - - - -
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Residues in contact with PHE 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LEU* 3.7 27.3 - - + +
109A LEU* 3.9 13.9 - - + -
110A ALA* 3.6 30.7 - - + -
113A VAL* 4.4 4.0 - - + -
143A VAL* 3.2 39.8 + - + -
144A ILE 3.8 0.9 - - - +
146A THR* 1.3 78.4 - - - +
148A ARG* 1.3 58.1 + - - +
150A TYR* 4.0 0.3 - - - +
151A ALA* 3.0 29.1 + - - +
193A PHE* 4.9 1.1 - + - -
194A ALA* 3.8 18.4 - - + -
197A ILE* 3.8 34.1 - - + -
198A ALA* 3.8 20.0 - - + -
222A MET* 3.9 20.6 - - + -
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Residues in contact with ARG 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ASP* 3.4 38.8 + - - +
110A ALA* 3.7 12.6 + - + +
111A ASP* 2.5 40.4 + - - +
114A GLU* 3.3 20.6 + - - -
144A ILE* 3.1 28.1 + - + +
145A LYS* 4.0 7.0 - - + +
147A PHE* 1.3 73.7 - - - +
149A TYR* 1.3 68.1 + - - +
151A ALA* 3.5 2.9 + - - +
152A GLY* 3.5 13.7 + - - -
104D ARG* 3.2 56.2 - - - +
156D LYS* 5.2 0.3 + - - -
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Residues in contact with TYR 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A LYS 2.8 18.6 + - - +
146A THR 3.6 3.1 - - - +
148A ARG* 1.3 77.4 - - - +
150A TYR* 1.3 91.0 + + - +
152A GLY 3.2 10.0 + - - -
153A TRP* 2.8 33.6 + + - -
479A ALA* 3.5 25.4 - - + -
480A GLN* 3.6 37.6 + - + +
496A GLY* 3.4 19.3 - - - -
497A GLU* 3.5 2.1 + - - +
155D ASP* 3.6 24.0 - - - +
156D LYS* 3.3 43.4 + - + +
158D HIS* 5.0 4.2 + - - -
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Residues in contact with TYR 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LEU* 4.0 5.2 - - + +
146A THR* 3.1 23.2 + - + +
147A PHE 4.4 0.4 - - - +
149A TYR* 1.3 90.2 - + - +
151A ALA* 1.3 66.9 + - - +
152A GLY 3.1 1.3 - - - -
153A TRP* 3.1 22.8 + + - +
154A ALA* 3.5 1.6 + - - +
198A ALA* 4.0 29.6 - - + +
199A PRO* 3.9 21.3 - - + +
202A CYS* 3.2 22.4 - - + +
495A MET* 3.1 48.1 + - + +
496A GLY 3.0 24.4 + - - -
499A GLY* 4.2 4.7 - - - -
500A LEU* 3.7 31.2 - - + -
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Residues in contact with ALA 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A GLY* 3.2 45.8 - - - +
106A LEU* 3.8 6.1 - - + +
107A ASP* 3.7 27.6 - - - +
147A PHE 3.0 20.4 + - - +
148A ARG 3.6 7.2 - - - +
150A TYR* 1.3 77.0 - - - +
152A GLY* 1.3 59.9 + - - +
153A TRP 3.5 0.2 + - - -
154A ALA* 3.6 5.7 + - - +
155A ASP* 5.1 1.6 + - - +
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Residues in contact with GLY 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A ARG 3.5 4.9 + - - -
149A TYR 3.2 9.3 + - - -
150A TYR 3.1 1.0 - - - -
151A ALA* 1.3 80.3 - - - +
153A TRP* 1.3 58.6 + - - +
154A ALA 3.3 0.4 + - - -
155A ASP* 3.6 1.9 - - - +
156A LYS* 2.7 34.6 + - - +
148D ARG 5.9 0.7 - - - -
152D GLY* 3.9 22.4 - - - -
156D LYS* 3.8 7.9 - - - -
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Residues in contact with TRP 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A TYR* 2.8 45.6 + + - -
150A TYR* 3.1 17.7 + + + +
152A GLY* 1.3 77.7 - - - +
154A ALA* 1.3 65.9 + - - +
155A ASP 3.3 0.7 - - - -
156A LYS* 2.9 49.7 + - + -
157A ILE* 3.4 13.4 + - - +
202A CYS* 3.4 19.3 - - - -
497A GLU* 3.5 49.9 - - + +
500A LEU* 3.7 20.0 - - + -
153D TRP* 4.5 12.3 - + - -
156D LYS* 3.4 37.9 - - + +
158D HIS* 4.2 7.2 - + - -
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Residues in contact with ALA 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ALA* 3.3 34.7 - - - +
100A SER* 5.1 0.4 - - - -
102A ARG* 3.8 11.6 + - + +
103A GLY* 3.6 17.7 - - - +
150A TYR 3.5 2.7 + - - +
151A ALA 3.8 8.1 - - - +
152A GLY 3.3 2.6 - - - -
153A TRP* 1.3 78.4 - - - +
155A ASP* 1.3 57.9 + - - +
156A LYS 3.6 0.5 + - - -
157A ILE* 4.1 9.8 + - - +
202A CYS* 3.6 28.7 - - - +
163B PRO* 4.4 3.1 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il